• Tuberculosis and Respiratory Diseases
• /
• v.76 no.2
• /
• pp.59-65
• /
• 2014

Background: Variable-number tandem repeat (VNTR) typing is a promising method to discriminate the Mycobacterium tuberculosis isolates in molecular epidemiology. The purpose of this study is to determine the optimal VNTR combinations for discriminating isolated M. tuberculosis strains in Korea. Methods: A total of 317 clinical isolates collected throughout Korea were genotyped by using the IS6110 restriction fragment length polymorphism (RFLP), and then analysed for the number of VNTR copies from 32 VNTR loci. Results: The results of discriminatory power according to diverse combinations were as follows: 25 clusters in 83 strains were yielded from the internationally standardized 15 VNTR loci (Hunter-Gaston discriminatory index [HGDI], 0.9958), 25 clusters in 65 strains by using IS6110 RFLP (HGDI, 0.9977), 14 clusters in 32 strains in 12 hyper-variable VNTR loci (HGDI, 0.9995), 6 clusters in 13 strains in 32 VNTR loci (HDGI, 0.9998), and 7 clusters in 14 strains of both the 12 hyper-variable VNTR and IS6110 RFLP (HDGI, 0.9999). Conclusion: The combination of 12 hyper-variable VNTR typing can be an effective tool for genotyping Korean M. tuberculosis isolates where the Beijing strains are predominant.

• Molecules and Cells
• /
• v.28 no.2
• /
• pp.87-92
• /
• 2009

Human SIRT3 gene contains an intronic VNTR enhancer. A T > C transition occurring in the second repeat of each VNTR allele implies the presence/absence of a putative GATA binding motif. A partially overlapping AP-1 site, not affected by the transition, was also identified. Aims of the present study were: 1) to verify if GATA and AP-1 sites could bind GATA2 and c-Jun/c-Fos factors, respectively; 2) to investigate whether such sites modulate the enhancer activity of the SIRT3-VNTR alleles. DAPA assay proved that GATA2 and c-Jun/c-Fos factors are able to bind the corresponding sites. Moreover, co-transfection experiments showed that the over-expression of GATA2 and c-Jun/c-Fos factors boosts the VNTR enhancer activity in an allelic-specific way. Furthermore, we established that GATA2 and c-Jun/c-Fos act additively in modulating the SIRT3-VNTR enhancer function. Therefore, GATA2 and AP-1 are functional sites and the T > C transition of the second VNTR repeat affects their activity.

• Journal of Sasang Constitutional Medicine
• /
• v.8 no.2
• /
• pp.151-163
• /
• 1996

VNTR and STR DNA typing are typical genetic analysis methods which are widely used in DNA-fingerprinting for forensic science and other genetic research purposes. In this study, genomic DNA of different constitutions(Taeun, Soyang and Soum) were analyzed by VNTR and STR DNA typing to provide scientific and objective references for Sasang Medicine. It was found out in this study that VNTR-MCT118 and YNZ22 loci showed too many different variation of allele distribution and numbers for each constitution. Therefore, it is thought that VNTR typing can not used for genetic classification study for Sasang Constitution which classifies human body into 4 groups. However, vWA locus, one of the STR loci investigated in this study, showed slight difference in allele distribution for each different constitution.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.2
• /
• pp.338-346
• /
• 2018

Two molecular epidemiologic methods, IS6110 restriction fragment length polymorphism (IS6110-RFLP) and 24-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR), are used worldwide in studies of Mycobacterium tuberculosis (MTB). Conversely, because of its poor resolution, pulsed-field gel electrophoresis (PFGE) is not widely used for MTB. In this study, we improved the 24-locus MIRU-VNTR and PFGE protocols and compared the effectiveness of these approaches for the molecular typing of MTB using 75 clinical isolates obtained from a cohort investigation of high-risk populations infected with MTB. The 24-locus MIRU-VNTR method demonstrated superior discriminatory ability, followed by PFGE and IS6110-RFLP. Next, we analyzed six isolates with clear epidemiologic connections; that is, isolates from patients who attended the same school. IS6110-RFLP and PFGE identified these samples as the same type. By contrast, according to MIRU-VNTR, two isolates differed from four other isolates at one locus each; one isolate was identified as Mtub29 and the other as QUB-26. In summary, the 24-locus MIRU-VNTR assay was the most useful molecular typing method among the three methods investigated due to its discriminatory power, short time required, and availability as an epidemiologic investigation tool. PFGE was the second-best method. Compared with the other loci assessed in the 24-locus MIRU-VNTR assay, the Mtub29 and QUB-26 loci appeared to exhibit greater variability during transmission.

• Korean Journal of Biological Psychiatry
• /
• v.25 no.1
• /
• pp.16-20
• /
• 2018

Objectives Psychological resilience is the ability to cope with stress. The genetic background behind psychological resilience is not much known. The serotonin transporter and dopamine transporter are implicated in stress related psychology and emotional processing. The aim of this study is to investigate a possible genetic role of functional polymorphisms of serotonin and dopamine transporters for psychological resilience. Methods A total of 951 healthy adult subjects were included. Psychological resilience was measured using Connor-Davidson Resilience Scale (CD-RISC). Genotyping was performed for serotonin transporter gene(SERT) promoter variable number tandem repeat (VNTR) and dopamine transporter gene(DAT1) 3'-untranslated region (UTR) VNTR. Genetic association analysis was conducted between genotypes and the CD-RISC score. Results No genetic association was observed for SERT promoter VNTR or DAT1 3'-UTR VNTR with CD-RISC score. No genetic interaction between SERT promoter VNTR and DAT1 3'-UTR VNTR with CD-RISC score was detected. Conclusions Either serotonin or dopamine transporter did not seem to play a significant role for psychological resilience in this sample.

• BMB Reports
• /
• v.28 no.4
• /
• pp.359-362
• /
• 1995

The highly polymorphic variable number of tandem repeat (VNTR) loci in the human genome are informative markers for the genetic characterization of individuals in the paternity test and forensic science as well as for the study of human disease. In this study, VNTR loci D1S80 and D2S123 have been amplified by PCR and the amplified length polymorphic alleles were detected with a discontinuous vertical PAGE system and silver staining. For explicit DNA typing, PCR optimization, in which amplification efficiencies are similar over a wide range of allele sizes, non-specific amplifications are minimal, and new longer alleles have high amplification efficiency, has been performed by changing the PCR reaction buffer composition and thermal cycling conditions. It turned out that adding an appropriate amount of Tween 20 and NP40 to the PCR reaction buffer and raising the annealing temperature to $68^{\circ}C$ in thermal cycling made it possible for optimal VNTR loci amplification. A modified PAGE system for VNTR separation was established. Under these conditions, new longer alleles in the 01580 locus were discovered and 025123 pattern changes in colorectal tumors were observed. These technical tips are valuable for detecting various amplified fragment length polymorphisms.

• 한국생물공학회:학술대회논문집
• /
• 2000.04a
• /
• pp.592-595
• /
• 2000

In human chromosome, a short sequence of DNA has been repeated a number of times. These repeats are called variable number of tandem repeat(VNTR) or short tandem repeat(STR) which has short repeat core. VNTR and STR are used in the field of forensic science, evolution, and anthropology. In this work, we examined allele frequencies of 3 VNTR(YNZ22, NeuR, D21S11) and one STR(Humth01) in a Korean population sample by polymerase chain reaction(PCR) followed by high-resolution polyacrylamide gelelectrophoresis(PAGE) with silver staining. Subsequently, the polymorphism information content(PIC) was calculated : the highest PIC was observed for the NeuR locus(0.95680) and lowest for the Humth01 locus(0.75809).

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.5 no.3
• /
• pp.169-173
• /
• 2000

On human chromoscomes, a short sequence of DNA is known to repeat a number of times. These are called variable number of tandem repeat (VNTR) or short tandem respeat (STR) which has a short core. VNTR and STR are used in the filed of forensic science, evolution, and anthropology. In this work, we examined allele frequencies of one VNTR (YNZ22) and three STRs (NeuR, D21S11, Humth01) in a korean population sample by polymerase chain reaction (RCP) followed by high-resolution polyacrylamide gel electro-phoresis (PAGE) with silver stain. Subsequently, the polymorphism information content (PIC) was calculated : the hifhest PIC was observed in the NeuR locus (0.95680) and lowest in the Humth01 locus (0.75809).

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.11
• /
• pp.5557-5562
• /
• 2012

Aim: The aim of this study was to investigate the frequency and correlation between auto-antibodies to survivin and MUC1 variable number tandem repeats (VNTR) in colorectal cancer (CRC), which can provide valuable information for the design of immunotherapeutic vaccines for this disease. Methods: Enzyme-linked immunosorbent assays (ELISA) were used to examine the level of auto-antibodies against survivin and MUC1 VNTR in the serum of 135 CRC patients and 95 healthy volunteers. Results: Using mean absorbance + 2 standard deviations (SD) of the healthy samples as a cut-off value, the positive rates of survivin and MUC1 VNTR auto-antibodies in CRC were 31.1% and 18.5%, respectively. Altogether, the survivin and MUC1 VNTR positive samples accounted for 36.3% of the CRC patients, and 7.4% were positive for both. Conclusion: A significant positive correlation was found between levels of specific antibodies against survivin and MUC1 VNTR in the serum of CRC patients (r = 0.3652, P < 0.0001), suggesting that vaccines against both targets would elicit immune responses more effectively.

• Sleep Medicine and Psychophysiology
• /
• v.15 no.1
• /
• pp.39-43
• /
• 2008

Objectives: The pathophysiology of restless legs syndrome (RLS) is not obvious, but many promising theories involve dopaminergic deficiency and genetic causes. The RLS is presumed to occur more frequently among schizophrenic patients who take antipsychotics, most of which blocks the dopamine receptors. This study aimed to investigate whether dopamine transporter gene (DAT1) 40 base pair (bp) variable number of tandem repeat (VNTR) polymorphism is associated with the antipsychotic-induced RLS in schizophrenia. Methods: We determined the diagnosis of RLS among the 190 Korean schizophrenic patients by the diagnostic criteria of the International Restless Legs Syndrome Study Group (IRLSSG). Genotyping was performed for the 40bp VNTR in DAT1 gene using polymerase chain reaction. Results: We separated the schizophrenic patients into 44 patients with RLS and 146 patients without RLS. The genotype and allele frequencies did not differ significantly between two groups. Conclusions: These results suggest that DAT1 gene 40bp VNTR is not associated with the antipsychotic-induced RLS in schizophrenia. To confirm these results, larger-scale association study is needed in the future.